X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.43
Temperature 277.0
Details 0.9500M sodium citrate, 0.1M sodium cacodylate pH 6.43, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 58.83 α = 90
b = 186.62 β = 103.06
c = 93.71 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2008-12-08
Diffraction Radiation
Monochromator Protocol
Double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 -- SSRL BL9-2

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2 30.03 97.0 0.056 -- -- 3.52 -- 131295 -- -3.0 26.888
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.0 2.07 90.0 0.346 -- 1.6 -- --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
SAD 2.0 30.029 -- 0.0 -- 131250 6601 99.26 -- 0.147 0.145 0.187 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.0 2.052 -- 460 8985 0.208 0.264 -- 96.86
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.557
Anisotropic B[1][1] 1.17
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.51
Anisotropic B[2][2] -0.54
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.05
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_other 0.196
r_nbtor_refined 0.187
r_dihedral_angle_4_deg 15.796
r_xyhbond_nbd_other 0.043
r_gen_planes_other 0.001
r_mcangle_it 3.078
r_angle_refined_deg 1.633
r_mcbond_other 0.541
r_chiral_restr 0.1
r_nbd_refined 0.229
r_nbtor_other 0.093
r_mcbond_it 1.855
r_xyhbond_nbd_refined 0.184
r_gen_planes_refined 0.006
r_scbond_it 5.847
r_dihedral_angle_2_deg 34.833
r_dihedral_angle_3_deg 12.549
r_angle_other_deg 0.995
r_metal_ion_refined 0.135
r_symmetry_hbond_refined 0.193
r_scangle_it 7.692
r_dihedral_angle_1_deg 4.772
r_symmetry_vdw_refined 0.093
r_bond_other_d 0.002
r_bond_refined_d 0.018
r_symmetry_vdw_other 0.31
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12909
Nucleic Acid Atoms 0
Heterogen Atoms 76
Solvent Atoms 865

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
PHENIX refinement
SHELX phasing
MolProbity model building version: 3beta29
XSCALE data scaling
PDB_EXTRACT data extraction version: 3.006
XDS data reduction
SHELXD phasing
autoSHARP phasing